Journal: Genes

Article Title: Comparing Transcriptome Profiles of Saccharomyces Cerevisiae Cells Exposed to Cadmium Selenide/Zinc Sulfide and Indium Phosphide/Zinc Sulfide

doi: 10.3390/genes12030428

Figure Lengend Snippet: Growth assay to determine growth rates of CdSe/ZnS and InP/ZnS-treated yeast cells. ( A , B ) Quantification of cell optical densities over a 24-h period where the cells are treated with CdSe/ZnS and InP/ZnS quantom dots (QDs), respectively, at 30 °C while shaking. ( C , D ) Measurement of cell optical densities at 24 h of treatment with CdSe/ZnS and InP/ZnS QDs, respectively. The bar representing the average optical densities (ODs) (594 nm) of each concentration at the 24-h mark. ( E , F ) Doubling time takes place during the phase of exponential growth for the cells treated with CdSe/ZnS and InP/ZnS QDs, respectively, and was measured as the amount of time it takes for cells to double their ODs. ( G , H ) The mean lag time before the exponential growth phase. Significant statistical differences are represented with *( p < 0.05), **( p < 0.01), and ***( p < 0.001).

Article Snippet: The emission wavelength of green-emitting CdSe/ZnS QDs were found to be 530–550 nm [ ] and InP/ZnS QDs 530 nm +/−15 nm (NNCrystal US Corporation, Fayetteville, AR, USA) (unpublished).

Techniques: Growth Assay, Concentration Assay

Journal: Genes

Article Title: Comparing Transcriptome Profiles of Saccharomyces Cerevisiae Cells Exposed to Cadmium Selenide/Zinc Sulfide and Indium Phosphide/Zinc Sulfide

doi: 10.3390/genes12030428

Figure Lengend Snippet: Bar graphs of the number of differentially expressed genes implicated in GO-terms that represent one specific cellular function altered when exposed to QDs in yeast. The number of differentially expressed genes (DEGs) on each bar represents the number of an altered gene for the corresponding GO-term with p -values of 0.05 or below. ( A ) The total number of upregulated DEGs implicated in the listed GO-terms in CdSe/ZnS-treated cells. ( B ) The total number of downregulated DEGs implicated in the listed GO-terms in CdSe/ZnS-treated cells. ( C ) The total number of upregulated DEGs implicated in the listed GO-terms in InP/ZnS-treated cells. ( D ) The total number of downregulated DEGs implicated in the listed GO-terms in InP/ZnS-treated cells.

Article Snippet: The emission wavelength of green-emitting CdSe/ZnS QDs were found to be 530–550 nm [ ] and InP/ZnS QDs 530 nm +/−15 nm (NNCrystal US Corporation, Fayetteville, AR, USA) (unpublished).

Techniques: Cell Function Assay

Journal: Genes

Article Title: Comparing Transcriptome Profiles of Saccharomyces Cerevisiae Cells Exposed to Cadmium Selenide/Zinc Sulfide and Indium Phosphide/Zinc Sulfide

doi: 10.3390/genes12030428

Figure Lengend Snippet: Gene expression ratios of ALG9 and one up- and downregulated gene from QD-treated samples determined by RT-qPCR. The reference gene ALG9 and other differentially expressed genes (from CdSe/ZnS and InP/ZnS-treated samples) were selected from our RNA-seq expression data and validated by determining their relative fold-change using the Pfaffl method. ( A ) Upregulated (TIR1) and downregulated (SPS100) genes with significantly altered gene expression levels Compared to ALG9 when treated with CdSe/ZnS. ( B ) Upregulated (HXK1) and downregulated (YDL012C) genes with significantly altered gene expression levels compared to ALG9 when treated with CdSe/ZnS. One asterisk (*) represents p < 0.05, while 4 asterisks (****) represent p < 0.0001.

Article Snippet: The emission wavelength of green-emitting CdSe/ZnS QDs were found to be 530–550 nm [ ] and InP/ZnS QDs 530 nm +/−15 nm (NNCrystal US Corporation, Fayetteville, AR, USA) (unpublished).

Techniques: Expressing, Quantitative RT-PCR, RNA Sequencing Assay

Journal: Genes

Article Title: Comparing Transcriptome Profiles of Saccharomyces Cerevisiae Cells Exposed to Cadmium Selenide/Zinc Sulfide and Indium Phosphide/Zinc Sulfide

doi: 10.3390/genes12030428

Figure Lengend Snippet: A table of genes implicated in antioxidant defense. It represents upregulated and downregulated genes in yeast exposed to CdSe/ZnS and InP/ZnS QDs. All genes incorporated in this table had p -values of 0.05 or below.

Article Snippet: The emission wavelength of green-emitting CdSe/ZnS QDs were found to be 530–550 nm [ ] and InP/ZnS QDs 530 nm +/−15 nm (NNCrystal US Corporation, Fayetteville, AR, USA) (unpublished).

Techniques:

Journal: Genes

Article Title: Comparing Transcriptome Profiles of Saccharomyces Cerevisiae Cells Exposed to Cadmium Selenide/Zinc Sulfide and Indium Phosphide/Zinc Sulfide

doi: 10.3390/genes12030428

Figure Lengend Snippet: Quantification of reactive oxygen species (ROS) levels including superoxide and peroxynitrite generated by cells treated with CdSe/ZnS and InP/ZnS QDs at 10 and 100 µg/mL, respectively. Samples were treated with and incubated with dihydroethidium (DHE) or dihydrorhodamine (DHR) 2 h prior to measuring the oxidized DHE and DHR fluorescent byproducts, which we measured with flow cytometry, that allow us to observe changes in superoxide and peroxynitrite levels generated in each QD-treatment, respectively. ( A ) Non-treated sample without DHE. ( B ) Non-treated sample dyed with DHE. ( C ) DHE dyed sample treated with 100 µg/mL CdSe/ZnS. ( D ) DHE dyed sample treated with 100 µg/mL InP/ZnS. ( E ) Bar graph comparing % changes in superoxide levels. ( F ) Non-treated sample without DHR. ( G ) Non-treated sample dyed with DHR. ( H ) DHR dyed sample treated with 100 µg/mL CdSe/ZnS. ( I ) DHR dyed sample treated with 100 µg/mL InP/ZnS. ( J ) Bar graphs comparing % changes in peroxynitrite levels. One asterisk represent p < 0.05 and four asterisk represent p < 0.0001.

Article Snippet: The emission wavelength of green-emitting CdSe/ZnS QDs were found to be 530–550 nm [ ] and InP/ZnS QDs 530 nm +/−15 nm (NNCrystal US Corporation, Fayetteville, AR, USA) (unpublished).

Techniques: Generated, Incubation, Flow Cytometry

Journal: Genes

Article Title: Comparing Transcriptome Profiles of Saccharomyces Cerevisiae Cells Exposed to Cadmium Selenide/Zinc Sulfide and Indium Phosphide/Zinc Sulfide

doi: 10.3390/genes12030428

Figure Lengend Snippet: A table that compares upregulated DEGs involved in cellular trafficking processes when exposed to green CdSe/ZnS and InP/ZnS QDs. The processes of interest include SNARE components, the Retromer, Sorting Nexin, and GARP complexes. All genes incorporated in this table had P-values of 0.05 or below.

Article Snippet: The emission wavelength of green-emitting CdSe/ZnS QDs were found to be 530–550 nm [ ] and InP/ZnS QDs 530 nm +/−15 nm (NNCrystal US Corporation, Fayetteville, AR, USA) (unpublished).

Techniques:

Journal: Genes

Article Title: Comparing Transcriptome Profiles of Saccharomyces Cerevisiae Cells Exposed to Cadmium Selenide/Zinc Sulfide and Indium Phosphide/Zinc Sulfide

doi: 10.3390/genes12030428

Figure Lengend Snippet: Cell images and bar graphs representing the number of Vps10-GFP puncta in CdSe/ZnS and InP/ZnS treated samples. ( A – D ) Representative images of wild type Vps10-GFP puncta in yeast. ( A ) Bar graph representing the average number of Vps10-GFP puncta per cell in CdSe/ZnS-treated samples. ( B ) Bar graph representing the average number of Vps10-GFP puncta per cell in InP/ZnS-treated samples. ( C ) Representative immunofluorescence image of a wild type Vps10-GFP cell from an NTC sample. ( D ) Representative immunofluorescence image of a cell from a sample treated with 10 µg/mL CdSe/ZnS. ( E ) Representative immunofluorescence image of a cell from a sample treated with 10 µg/mL InP/ZnS. ( F ) Bar graph representing the average number of Vps10-GFP puncta per cell in InP/ZnS-treated samples. Two asterisks represent p < 0.01 and four asterisks represent p < 0.0001.

Article Snippet: The emission wavelength of green-emitting CdSe/ZnS QDs were found to be 530–550 nm [ ] and InP/ZnS QDs 530 nm +/−15 nm (NNCrystal US Corporation, Fayetteville, AR, USA) (unpublished).

Techniques: Immunofluorescence

Journal: Genes

Article Title: Comparing Transcriptome Profiles of Saccharomyces Cerevisiae Cells Exposed to Cadmium Selenide/Zinc Sulfide and Indium Phosphide/Zinc Sulfide

doi: 10.3390/genes12030428

Figure Lengend Snippet: Detailed schematic models representing changes in cellular processes with CdSe/ZnS QDs or InP/ZnS QDs in the budding yeast. Cellular processes are illustrated and labeled with the genes involved and whose normal regulation has been up or downregulated. ( A ) CdSe/ZnS QD exposure causes an increase in the expression of genes involved in cellular processes such as transmembrane transport/cellular homeostasis, vacuole acidification, amino acid metabolic activity, protein folding, and trafficking within the trans -Golgi network. ( B ) Decreased expression in many genes treated with CdSe/ZnS has revealed many important downregulated processes involved in endocytosis, the Cvt pathway, rRNA processing, proteasome assembly, metabolic activity, cell cycle regulation, and trafficking within the trans -Golgi network. ( C ) Yeast exposed to InP/ZnS QDs has upregulated many genes required for processes like endocytosis, peroxisome assembly, proteasome assembly and activity, the Cvt pathway, the ETC, and oxido-reduction metabolic processes. ( D ) Several more processes are downregulated when exposed to InP/ZnS QDs including endocytosis, rRNA processing, translation, the Cvt pathway, actin and microtubule growth, vesicle fusion, and protein targeting to the plasma membrane, and some trans -Golgi network trafficking.

Article Snippet: The emission wavelength of green-emitting CdSe/ZnS QDs were found to be 530–550 nm [ ] and InP/ZnS QDs 530 nm +/−15 nm (NNCrystal US Corporation, Fayetteville, AR, USA) (unpublished).

Techniques: Labeling, Expressing, Activity Assay

Journal: Genes

Article Title: Comparing Transcriptome Profiles of Saccharomyces Cerevisiae Cells Exposed to Cadmium Selenide/Zinc Sulfide and Indium Phosphide/Zinc Sulfide

doi: 10.3390/genes12030428

Figure Lengend Snippet: A table listing the GO-terms and genes in Figure 6 A. It represents the multiple upregulated cellular processes and genes in yeast exposed to 10 µg/mL CdSe/ZnS QDs. All genes incorporated in this table exhibited expression levels significantly higher than expression levels of NTC samples.

Article Snippet: The emission wavelength of green-emitting CdSe/ZnS QDs were found to be 530–550 nm [ ] and InP/ZnS QDs 530 nm +/−15 nm (NNCrystal US Corporation, Fayetteville, AR, USA) (unpublished).

Techniques: Expressing, Activity Assay

Journal: Genes

Article Title: Comparing Transcriptome Profiles of Saccharomyces Cerevisiae Cells Exposed to Cadmium Selenide/Zinc Sulfide and Indium Phosphide/Zinc Sulfide

doi: 10.3390/genes12030428

Figure Lengend Snippet: A table listing the GO-terms and genes in Figure 6 B. It represents the multiple downregulated cellular processes and genes in yeast exposed to 10 µg/mL CdSe/ZnS QDs. All genes incorporated in this table exhibited expression levels significantly lower than expression levels of NTC samples.

Article Snippet: The emission wavelength of green-emitting CdSe/ZnS QDs were found to be 530–550 nm [ ] and InP/ZnS QDs 530 nm +/−15 nm (NNCrystal US Corporation, Fayetteville, AR, USA) (unpublished).

Techniques: Expressing, Activity Assay

Journal: Genes

Article Title: Comparing Transcriptome Profiles of Saccharomyces Cerevisiae Cells Exposed to Cadmium Selenide/Zinc Sulfide and Indium Phosphide/Zinc Sulfide

doi: 10.3390/genes12030428

Figure Lengend Snippet: A proportionately accurate Venn-diagram that represents the number of up- and downregulated genes whose expression has been significantly changed when exposed to CdSe/ZnS QDs or InP/ZnS QDs. The overlapped segments of each Venn-diagram represent genes that are differentially expressed when exposed to CdSe/ZnS and InP/ZnS QDs. The portions of the Venn-diagram that do not overlap are up- or downregulated genes that become differentially expressed only when exposed to CdSe/ZnS QDs or InP/ZnS QDs. ( A ) Every gene whose expression was significantly increased when compared to the normal gene expression in yeast cells when exposed to CdSe/ZnS or InP/ZnS QDs. ( B ) Every gene whose expression was significantly decreased when exposed to CdSe/ZnS or InP/ZnS QDs.

Article Snippet: The emission wavelength of green-emitting CdSe/ZnS QDs were found to be 530–550 nm [ ] and InP/ZnS QDs 530 nm +/−15 nm (NNCrystal US Corporation, Fayetteville, AR, USA) (unpublished).

Techniques: Expressing

Journal: Genes

Article Title: Comparing Transcriptome Profiles of Saccharomyces Cerevisiae Cells Exposed to Cadmium Selenide/Zinc Sulfide and Indium Phosphide/Zinc Sulfide

doi: 10.3390/genes12030428

Figure Lengend Snippet: A table listing the GO-terms and genes in Figure 6 C. It represents the multiple upregulated cellular processes and genes in yeast exposed to 100 µg/mL InP/ZnS QDs. All genes incorporated in this table exhibited expression levels significantly higher than expression levels of NTC samples.

Article Snippet: The emission wavelength of green-emitting CdSe/ZnS QDs were found to be 530–550 nm [ ] and InP/ZnS QDs 530 nm +/−15 nm (NNCrystal US Corporation, Fayetteville, AR, USA) (unpublished).

Techniques: Expressing, Activity Assay

Journal: Genes

Article Title: Comparing Transcriptome Profiles of Saccharomyces Cerevisiae Cells Exposed to Cadmium Selenide/Zinc Sulfide and Indium Phosphide/Zinc Sulfide

doi: 10.3390/genes12030428

Figure Lengend Snippet: A table listing the GO-terms and genes in Figure 6 D. It represents the multiple downregulated cellular processes and genes in yeast exposed to 100 µg/mL InP/ZnS QDs. All genes incorporated in this table exhibited expression levels significantly lower than expression levels of NTC samples.

Article Snippet: The emission wavelength of green-emitting CdSe/ZnS QDs were found to be 530–550 nm [ ] and InP/ZnS QDs 530 nm +/−15 nm (NNCrystal US Corporation, Fayetteville, AR, USA) (unpublished).

Techniques: Expressing